Unable to get mask from hmm align result file... still problematic about gtdbtk HOT 10 CLOSED

Have you been able to resolve this issue?

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I haven't been able to resolve this issue.

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Can you make sure HMMer is on your path. Specifically, hmmscan. Can you also try setting the min_perc_aa parameter to 1? Perhaps your genome doesn't have any marker genes and this is causing the issue.

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This is contained in my .bashrc file:

export PATH="/nfs/vedanta/sw/packages/hmmer-3.2.1/bin:$PATH"

My colleague was able to successfully run the software on our cluster with the same genome dataset I am using, so I am unsure about the issue.

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We are currently using HMMer 3.1b. Is your colleague also using this previous version of HMMer? We will test out the new version at some point, but it will likely take a bit of time.

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We are using the same hmmer version.

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I'm not sure I can provide any more assistance on this end. It would appear GTDB-Tk works as expected and it is an installation/configuration issue on your system. I would recommend running each of the dependencies separately just to ensure they run and are properly on your system path. Please let me know if you resolve the issue as it may be useful knowledge to pass along to others.

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Thanks for you help. This issue does warrant more troubleshooting on our system. I suppose the next step is to see if another colleague can run the software on our system.

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By the way, we are quite excited about your software/method.

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Hope you get it running soon.

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